Merge pull request #755 from effigies/mnt/deprecations

MAINT: Effect FutureWarnings, including deprecations

Author: effigies

nibabel/__init__.py

@@ -77,7 +77,7 @@ def setup_test():
                            flip_axis, OrientationError,
                            apply_orientation, aff2axcodes)
 from .imageclasses import class_map, ext_map, all_image_classes
-from . import trackvis
+trackvis = _ModuleProxy('nibabel.trackvis')
 from . import mriutils
 from . import streamlines
 from . import viewers

nibabel/checkwarns.py

@@ -13,25 +13,20 @@
 import warnings
 
 from .testing import (error_warnings, suppress_warnings)
+from .deprecated import deprecate_with_version
 
 
 warnings.warn('The checkwarns module is deprecated and will be removed '
-              'in nibabel v3.0', FutureWarning)
+              'in nibabel v3.0', DeprecationWarning)
 
 
+@deprecate_with_version('ErrorWarnings is deprecated; use nibabel.testing.error_warnings.',
+                        since='2.1.0', until='3.0.0')
 class ErrorWarnings(error_warnings):
-
-    def __init__(self, *args, **kwargs):
-        warnings.warn('ErrorWarnings is deprecated and will be removed in '
-                      'nibabel v3.0; use nibabel.testing.error_warnings.',
-                      FutureWarning)
-        super(ErrorWarnings, self).__init__(*args, **kwargs)
+    pass
 
 
+@deprecate_with_version('IgnoreWarnings is deprecated; use nibabel.testing.suppress_warnings.',
+                        since='2.1.0', until='3.0.0')
 class IgnoreWarnings(suppress_warnings):
-
-    def __init__(self, *args, **kwargs):
-        warnings.warn('IgnoreWarnings is deprecated and will be removed in '
-                      'nibabel v3.0; use nibabel.testing.suppress_warnings.',
-                      FutureWarning)
-        super(IgnoreWarnings, self).__init__(*args, **kwargs)
+    pass

nibabel/minc.py

@@ -2,9 +2,9 @@
 
 import warnings
 
-warnings.warn("We will remove this module from nibabel soon; "
+warnings.warn("We will remove this module from nibabel 3.0; "
               "Please use the 'minc1' module instead",
-              FutureWarning,
+              DeprecationWarning,
               stacklevel=2)
 
 from .minc1 import *  # noqa

nibabel/minc1.py

@@ -18,7 +18,7 @@
 from .fileslice import canonical_slicers
 
 from .keywordonly import kw_only_meth
-from .deprecated import FutureWarningMixin
+from .deprecated import deprecate_with_version
 
 _dt_dict = {
     ('b', 'unsigned'): np.uint8,
@@ -331,13 +331,13 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
 
 
 # Backwards compatibility
-class MincFile(FutureWarningMixin, Minc1File):
-    """ Deprecated alternative name for Minc1File
-    """
-    warn_message = 'MincFile is deprecated; please use Minc1File instead'
+@deprecate_with_version('MincFile is deprecated; please use Minc1File instead',
+                        since='2.0.0', until='3.0.0', warn_class=FutureWarning)
+class MincFile(Minc1File):
+    pass
 
 
-class MincImage(FutureWarningMixin, Minc1Image):
-    """ Deprecated alternative name for Minc1Image
-    """
-    warn_message = 'MincImage is deprecated; please use Minc1Image instead'
+@deprecate_with_version('MincImage is deprecated; please use Minc1Image instead',
+                        since='2.0.0', until='3.0.0', warn_class=FutureWarning)
+class MincImage(Minc1Image):
+    pass

nibabel/testing/__init__.py

@@ -16,11 +16,13 @@
 from os.path import dirname, abspath, join as pjoin
 
 import numpy as np
-from numpy.testing import assert_array_equal
+from numpy.testing import assert_array_equal, assert_warns
 from numpy.testing import dec
 skipif = dec.skipif
 slow = dec.slow
 
+from ..deprecated import deprecate_with_version as _deprecate_with_version
+
 # Allow failed import of nose if not now running tests
 try:
     from nose.tools import (assert_equal, assert_not_equal,
@@ -187,12 +189,11 @@ class suppress_warnings(error_warnings):
     filter = 'ignore'
 
 
+@_deprecate_with_version('catch_warn_reset is deprecated; use '
+                         'nibabel.testing.clear_and_catch_warnings.',
+                         since='2.1.0', until='3.0.0')
 class catch_warn_reset(clear_and_catch_warnings):
-
-    def __init__(self, *args, **kwargs):
-        warnings.warn('catch_warn_reset is deprecated and will be removed in '
-                      'nibabel v3.0; use nibabel.testing.clear_and_catch_warnings.',
-                      FutureWarning)
+    pass
 
 
 EXTRA_SET = os.environ.get('NIPY_EXTRA_TESTS', '').split(',')

nibabel/tests/test_checkwarns.py

@@ -1,21 +1,11 @@
 """ Tests for warnings context managers
 """
-from __future__ import division, print_function, absolute_import
-
-from nose.tools import assert_equal
-from ..testing import clear_and_catch_warnings, suppress_warnings
+from ..testing import assert_equal, assert_warns, suppress_warnings
 
 
 def test_ignore_and_error_warnings():
     with suppress_warnings():
         from .. import checkwarns
 
-    with clear_and_catch_warnings() as w:
-        checkwarns.IgnoreWarnings()
-        assert_equal(len(w), 1)
-        assert_equal(w[0].category, FutureWarning)
-
-    with clear_and_catch_warnings() as w:
-        checkwarns.ErrorWarnings()
-        assert_equal(len(w), 1)
-        assert_equal(w[0].category, FutureWarning)
+    assert_warns(DeprecationWarning, checkwarns.IgnoreWarnings)
+    assert_warns(DeprecationWarning, checkwarns.ErrorWarnings)

nibabel/tests/test_minc1.py

@@ -24,10 +24,9 @@
 from .. import minc1
 from ..minc1 import Minc1File, Minc1Image, MincHeader
 
-from nose.tools import (assert_true, assert_equal, assert_false, assert_raises)
-from numpy.testing import assert_array_equal
 from ..tmpdirs import InTemporaryDirectory
-from ..testing import data_path
+from ..testing import (assert_true, assert_equal, assert_false, assert_raises, assert_warns,
+                       assert_array_equal, data_path, clear_and_catch_warnings)
 
 from . import test_spatialimages as tsi
 from .test_fileslice import slicer_samples
@@ -106,7 +105,8 @@ def test_old_namespace():
     # Check warnings raised
     arr = np.arange(24).reshape((2, 3, 4))
     aff = np.diag([2, 3, 4, 1])
-    with warnings.catch_warnings(record=True) as warns:
+    with clear_and_catch_warnings() as warns:
+        warnings.simplefilter('always', DeprecationWarning)
         # Top level import.
         # This import does not trigger an import of the minc.py module, because
         # it's the proxy object.
@@ -122,7 +122,9 @@ def test_old_namespace():
         # depending on whether the minc.py module is already imported in this
         # test run.
         if not previous_import:
-            assert_equal(warns.pop(0).category, FutureWarning)
+            assert_equal(warns.pop(0).category, DeprecationWarning)
+
+    with clear_and_catch_warnings() as warns:
         from .. import Minc1Image, MincImage
         assert_equal(warns, [])
         # The import from old module is the same as that from new
@@ -132,17 +134,17 @@ def test_old_namespace():
         assert_equal(warns, [])
         # Create object using old name
         mimg = MincImage(arr, aff)
-        assert_array_equal(mimg.get_data(), arr)
         # Call to create object created warning
         assert_equal(warns.pop(0).category, FutureWarning)
+        assert_array_equal(mimg.get_data(), arr)
         # Another old name
         from ..minc1 import MincFile, Minc1File
         assert_false(MincFile is Minc1File)
         assert_equal(warns, [])
         mf = MincFile(netcdf_file(EG_FNAME))
-        assert_equal(mf.get_data_shape(), (10, 20, 20))
         # Call to create object created warning
         assert_equal(warns.pop(0).category, FutureWarning)
+        assert_equal(mf.get_data_shape(), (10, 20, 20))
 
 
 class _TestMincFile(object):

nibabel/tests/test_removalschedule.py

@@ -0,0 +1,34 @@
+from ..info import cmp_pkg_version
+from ..testing import assert_raises, assert_false
+
+MODULE_SCHEDULE = [
+    ('4.0.0', ['nibabel.trackvis']),
+    ('3.0.0', ['nibabel.minc', 'nibabel.checkwarns']),
+    # Verify that the test will be quiet if the schedule outlives the modules
+    ('1.0.0', ['nibabel.neverexisted']),
+    ]
+
+OBJECT_SCHEDULE = [
+    ('3.0.0', [('nibabel.testing', 'catch_warn_reset')]),
+    # Verify that the test will be quiet if the schedule outlives the modules
+    ('1.0.0', [('nibabel', 'neverexisted')]),
+    ]
+
+
+def test_module_removal():
+    for version, to_remove in MODULE_SCHEDULE:
+        if cmp_pkg_version(version) < 1:
+            for module in to_remove:
+                with assert_raises(ImportError, msg="Time to remove " + module):
+                    __import__(module)
+
+
+def test_object_removal():
+    for version, to_remove in OBJECT_SCHEDULE:
+        if cmp_pkg_version(version) < 1:
+            for module_name, obj in to_remove:
+                try:
+                    module = __import__(module_name)
+                except ImportError:
+                    continue
+                assert_false(hasattr(module, obj), msg="Time to remove %s.%s" % (module_name, obj))

nibabel/tests/test_trackvis.py

@@ -10,9 +10,9 @@
 from ..orientations import aff2axcodes
 from ..volumeutils import native_code, swapped_code
 
-from nose.tools import assert_true, assert_false, assert_equal, assert_raises
-from numpy.testing import assert_array_equal, assert_array_almost_equal
-from ..testing import error_warnings, suppress_warnings
+from numpy.testing import assert_array_almost_equal
+from ..testing import (assert_true, assert_false, assert_equal, assert_raises, assert_warns,
+                       assert_array_equal, suppress_warnings)
 
 
 def test_write():
@@ -217,8 +217,7 @@ def _rt(streams, hdr, points_space):
             assert_raises(tv.HeaderError, tv.read, out_f, False, 'voxel')
         # There's a warning for any voxel sizes == 0
         hdr = {'voxel_size': [2, 3, 0]}
-        with error_warnings():
-            assert_raises(UserWarning, _rt, vx_streams, hdr, 'voxel')
+        assert_warns(UserWarning, _rt, vx_streams, hdr, 'voxel')
         # This should be OK
         hdr = {'voxel_size': [2, 3, 4]}
         (raw_streams, hdr), (proc_streams, _) = _rt(vx_streams, hdr, 'voxel')
@@ -305,9 +304,8 @@ def test__check_hdr_points_space():
                   tv._check_hdr_points_space, hdr, 'voxel')
     # Warning here only
     hdr['voxel_size'] = [2, 3, 0]
-    with error_warnings():
-        assert_raises(UserWarning,
-                      tv._check_hdr_points_space, hdr, 'voxel')
+    assert_warns(UserWarning,
+                 tv._check_hdr_points_space, hdr, 'voxel')
     # This is OK
     hdr['voxel_size'] = [2, 3, 4]
     assert_equal(tv._check_hdr_points_space(hdr, 'voxel'), None)
@@ -370,10 +368,6 @@ def test_empty_header():
 def test_get_affine():
     # Test get affine behavior, including pending deprecation
     hdr = tv.empty_header()
-    # Using version 1 affine is not a good idea because is fragile and not
-    # very useful. The default atleast_v2=None mode raises a FutureWarning
-    with error_warnings():
-        assert_raises(FutureWarning, tv.aff_from_hdr, hdr)
     # testing the old behavior
     old_afh = partial(tv.aff_from_hdr, atleast_v2=False)
     # default header gives useless affine
@@ -421,9 +415,8 @@ def test_get_affine():
         assert_equal(hdr['voxel_order'], o_codes)
         # Check it came back the way we wanted
         assert_array_equal(old_afh(hdr), in_aff)
-    # Check that the default case matches atleast_v2=False case
-    with suppress_warnings():
-        assert_array_equal(tv.aff_from_hdr(hdr), flipped_aff)
+    # Check that v1 header raises error
+    assert_raises(tv.HeaderError, tv.aff_from_hdr, hdr)
     # now use the easier vox_to_ras field
     hdr = tv.empty_header()
     aff = np.eye(4)
@@ -455,15 +448,7 @@ def test_aff_to_hdr():
     # Historically we flip the first axis if there is a negative determinant
     assert_array_almost_equal(hdr['voxel_size'], [-1, 2, 3])
     assert_array_almost_equal(tv.aff_from_hdr(hdr, atleast_v2=False), aff2)
-    # Test that default mode raises DeprecationWarning
-    with error_warnings():
-        assert_raises(FutureWarning, tv.aff_to_hdr, affine, hdr)
-        assert_raises(FutureWarning, tv.aff_to_hdr, affine, hdr, None, None)
-        assert_raises(FutureWarning, tv.aff_to_hdr, affine, hdr, False, None)
-        assert_raises(FutureWarning, tv.aff_to_hdr, affine, hdr, None, False)
-    # And has same effect as above
-    with suppress_warnings():
-        tv.aff_to_hdr(affine, hdr)
+    tv.aff_to_hdr(affine, hdr, pos_vox=False, set_order=False)
     assert_array_almost_equal(tv.aff_from_hdr(hdr, atleast_v2=False), affine)
     # Check pos_vox and order flags
     for hdr in ({}, {'version': 2}, {'version': 1}):
@@ -515,13 +500,6 @@ def test_tv_class():
     affine = np.diag([1, 2, 3, 1])
     affine[:3, 3] = [10, 11, 12]
     # affine methods will raise same warnings and errors as function
-    with error_warnings():
-        assert_raises(FutureWarning, tvf.set_affine, affine)
-        assert_raises(FutureWarning, tvf.set_affine, affine, None, None)
-        assert_raises(FutureWarning, tvf.set_affine, affine, False, None)
-        assert_raises(FutureWarning, tvf.set_affine, affine, None, False)
-        assert_raises(FutureWarning, tvf.get_affine)
-        assert_raises(FutureWarning, tvf.get_affine, None)
     tvf.set_affine(affine, pos_vox=True, set_order=True)
     aff = tvf.get_affine(atleast_v2=True)
     assert_array_almost_equal(aff, affine)